Identification and sequencing of the HLA-B*4106 allele

We report a novel HLA-B*41 allele (HLA-B*4106) initially detected by an unusual sequence-specific oligonucleotide (SSO) hybridization pattern and identified by sequence-based HLA typing. Molecular cloning and sequencing determined that the new HLA-B allele was identical to the HLA-B*4101 in exon 2 and 3 except for a single nucleotide substitution in the exon 3 changing codon 204 from Glu to Gln (GAG-->CAG). In addition, intron 2 was identical to the published HLA-B*4104 intron 2, except for the base 509 (C-->G).     

Identification of a novel HLA-B*2722 allele from a Filipino cell

We present the novel HLA-allele B*2722 amplified and sequenced from a Filipino individual. This DNA was included several times in the International Cell Exchange, UCLA, and typed at the time as B*27 or B*2706 by the majority of the participating laboratories. The second HLA-B allele of this person is B*3802. B*2704/06 or B*2704/06/10 were suggested by approximately one-third of the laboratories. As we were investigating the intron 3 sequences of B*27 alleles, we also sequenced exon 4 of this Filipino DNA and found a single nucleotide exchange in exon 4 (pos. 704) which was not in concordance with the previous B*2706 typing. Our sequencing results showed that the coding sequence of B*2722 is identical to B*2706 in exon 1, 2 and 3. In exon 4 the B*2722 sequence is identical to B*2704. HLA-B*2704 differs from B*2706 in one base at position 704, a G in B*2704 and a C in B*2706, respectively.     

Identification of a new HLA-B allele (B*1576) by haplotype specific extraction

Routine typing of a potential bone marrow donor by sequence-specific oligonucleotide probes (SSOP) and sequence based typing (SBT) produced inconclusive subtyping results, suggesting a new allele. A magnetic bead-based method, haplotype specific extraction (HSE), was used to separate the diploid sample into its haploid components. The sample was then re-typed using standard SBT, revealing a new human leukocyte antigen (HLA) allele, since named B*1576. HSE used in conjunction with standard SBT is a convenient and simple tool for resolving ambiguous and novel allele combinations without the need for amplification or subcloning.     

Development of a sensitive and specific nanoparticle-assisted PCR assay for detecting HPV-16 and HPV-18 DNA

Carcinoma precursor lesion caused by persistent infection of human papillomavirus (HPV) types 16 and 18 is known as a principal inducer of cervical cancer. Therefore, rapid and effective detection of HPV-16 and HPV-18 infection at early stage is an important strategy for preventing such disease. In this study, a novel duplex nanoparticle-assisted polymerase chain reaction (nanoPCR) assay was developed to detect both of the two genotypes simultaneously. Two pairs of primers for nanoPCR were designed based on the conserved region within the early 6 (E6) gene of HPV-16 and HPV-18, respectively. After optimizing reaction conditions, the nanoPCR assay displayed 10-fold more sensitive than that of conventional PCR and showed high specificity. The detection limit of nanoPCR was 1.7 × 10¹ copies/μL for HPV-16, 1.2 × 10² copies/μL for HPV-18, and no cross-reaction was detected after using other viruses or HPV subtypes as templates. Of 209 clinical samples collected from patients, as also confirmed by sequencing, the nanoPCR method gave consistent results with conventional PCR assay: 7 positives for HPV-16, 4 positives for HPV-18, and no co-infection. Here is the first report to introduce a reproducible nanoPCR assay for detecting HPV DNA with high sensitivity and specificity, which may point out a useful diagnostic tool for potential clinical application.     

Identification of a new HLA-DRB1 allele, HLA-DRB1*1212, and confirmation of HLA-B*1586*

A novel allele, HLA-DRB1*1212, was identified by sequence-based typing. DRB1*1212 was identical to DRB*120101 at exon 2 except for a single nucleotide at position 199 from A to C, leading to amino acidic substitution from Ile to Leu at codon 67. We also confirmed the HLA-B*1586 in another Chinese person.     

一例新的HLA-B等位基因B*5614的核苷酸序列分析

目的 研究HLA新的等位基因HLA-B*5614的分子基础。方法 样本DNA抽提采用盐析法，利用PCR方法扩增先证者HLA-B基因的第2～4外显子，PCR产物直接经TOPO转染克隆到质粒载体中分离其等位基因，对所得克隆进行第2～4外显子双向测序分析。应用序列特异性引物PCR方法证实测序所发现的突变。结果 先证者样本克隆测序得到两个等位基因，其中1个等位基因为B*1502，另一个经BLAST验证为新的等位基因，新的等位基因序列已递交GenBank(AY601726，AY601727，AY601728)。与最接近的B*5608等位基因序列相比，新的等位基因仅在第2外显子上有1个核苷酸不同，即第277位G→C，导致第93位氨基酸Cly→Arg。结论 该等位基因为新的HLA-B等位基因，被世界卫生组织HLA因子命名委员会正式命名为HLA-B*5614。     

Identification of two new HLA-B22 variants, HLA-B*5509 and B*5606

In our recent study using high-resolution HLA-B locus typing by sequence-based typing (SBT) we identified 9 new alleles in a total of 355 unrelated individuals (4). Three of them concerned an allele belonging to the B22 group. One of them, B*5607, showed the unusual presence of a Bw4 sequence motif, as described previously (5). In this report the other two B22 variants are described; one belonging to the B55 specificity and named B*5509; the other one being a B*56 allele and assigned B*5606, which brings the total number of alleles belonging to the B22 group to 18.     

Identification of two new HLA-B alleles, HLA-B*0732 and HLA-B*5809, by sequence-based typing

Here, we have described the characterization of two novel human leukocyte antigen-B (HLA-B) alleles. The new alleles, HLA-B*0732 and HLA-B*5809, were identified in Italian Caucasian individuals. B*0732 differs from HLA-B*0708 by one nucleotidic change at position 412 (from G to A) in exon 3, leading to an amino acidic substitution from Asp (GAC) to Asn (AAC) at codon 114. The sequence of B*5809 is identical to that of HLA-B*5801, except for a point mutation at position 583 in exon 3, where a T is substituted by a C. This change leads to an amino acidic substitution from Tyr (TAC) to His (CAC) at codon 171.     

Full length sequence of a novel HLA-B*3818 allele differs from HLA-B*380201 allele in exon 4 and intron 5

The full length sequence of HLA-B*3818 differs from HLA-B*380201 at nt 660 in exon 4 (C→A) and genomic position 2133 in intron 5 (A→C).     

Identification in humans of HPV-16 E6 and E7 protein epitopes recognized by cytolytic T lymphocytes in association with HLA-B18 and determination of the HLA-B18-specific binding motif

Human papilloma virus type 16 (HPV-16) is the HPV most frequently associated with cervical carcinoma in humans. For the prevention or treatment of cervical carcinoma, the E6 and E7 oncoproteins appear to be good targets for vaccine-induced cytotoxic T lymphocytes (CTL). Lipopeptide vaccination is an efficient way of stimulating cellular responses. However, to synthesize effective lipopeptides, it is necessary to define which epitopes are immunogenic. In this study we first determined that peptide 80 - 88 of the E6 protein was recognized by CTL from a healthy donor in association with the HLA-B18 molecule. We then defined the HLA-B18 anchoring peptide motif by testing the binding of various short peptides with the HLA-B18 molecule and showed that it was related to the HLA-A1-specific peptide motif. Furthermore, in analyzing the potential E7 epitopes susceptible to associating with HLA-B18, we demonstrated that peptide E7 44 - 52 gave the strongest binding. It could also be recognized by CTL from peripheral blood mononuclear cells (PBMC) of the same healthy donor. Finally, with PBMC from a patient with a cervical intraepithelial neoplasia grade 3, we found CTL which recognized the E6 80 - 88 epitope. We have hence identified two peptides encoded by the E6 and E7 proteins which are presented by the HLA-B18 molecule and could be included in a vaccine against HPV-16.     

Identification of a novel HLA-B*15 allele, B*9529, in the Chinese population

We report here the identification of a novel human leukocyte antigen-B*9529 allele that was detected by polymerase chain reaction sequence-based typing.     

A single amino acid change makes the peptide specificity of B*3910 unrelated to B*3901 and closer to a group of HLA-B proteins including the malaria-protecting allotype HLA-B53

Abstract: HLA-B*3910, which has only been found in African and African American individuals, differs from B*3901 by the single amino acid change of Cys67 to Tyr67. Sequence analysis of the B*3910-bound peptide pool and of several individual ligands revealed that this subtype has strong preference for peptides with Pro2. This is in contrast with the preference of B*3901 for peptides with basic residues (Arg and His) at this position, and indicates that the single amino acid substitution between B*3910 and B*3901 totally changes the repertoire of bound peptides. This is presumably due to the significant decrease in the size of the B pocket, and to its increased hydrophobicity, since Tyr67 takes part in this pocket. B*3910 is similar to various other class I proteins in its preference for peptides with Pro2 and nonpolar C-terminal residues, including HLA-B53, an antigen associated with protection against severe malaria. The role of these two motifs as major peptidic anchors suggests that B*3910 and HLA-B53 may bind common peptides.     

Characterization of a new HLA-B allele, HLA-B*5312, and re-evaluation of the published sequences of the untranslated regions of HLA-B*35 and HLA-B*53

We report a novel human leukocyte antigen (HLA)-B allele, HLA-B*5312. Compared with HLA-B*530101, there is one silent substitution at nucleotide 438 and two non-synonymous substitutions at nucleotides 431 and 440, causing a change of the amino acid sequence (Asn-->Ser at codon 77 and Ile-->Thr at codon 80, respectively) within the Bw4 epitope. In contrast to the published sequences (IMGT/HLA Database, version 2.16.0, January 2007), we found that HLA-B*530101 had a C instead of a T at nucleotide -221, whereas HLA-B*350101 had a C instead of an A at nucleotide 2992. According to our sequencing results, HLA-B*5312 resembles HLA-B*350101 regarding its sequence of the untranslated regions. HLA-B*5312 may have been the result of a double crossing over event during which HLA-B*350101 adopted a Bw4 motif.     

Identification of a novel HLA-B allele, HLA-B*3580, with possible implication in transplantation and CTL response

A new human leukocyte antigen (HLA)-B allele, named B*3580, with an amino acid substitution at residue 156, has been identified during the sequence-based typing of a patient waiting for a hematopoietic cell transplantation.